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Q9LTX3

- PPOX1_ARATH

UniProt

Q9LTX3 - PPOX1_ARATH

Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic

Gene

PPOX1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 102 (01 Oct 2014)
      Sequence version 1 (01 Oct 2000)
      Previous versions | rss
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    Functioni

    Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). Involved in the PLP salvage pathway. Has a higher preference for PNP over PMP. May also catalyze the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S-specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX.2 Publications

    Catalytic activityi

    Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2.
    Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.
    (R)-NADHX = (S)-NADHX.

    Cofactori

    Binds 1 FMN per subunit.By similarity
    Binds 1 potassium ion per subunit.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi132 – 1321PotassiumBy similarity
    Metal bindingi196 – 1961PotassiumBy similarity
    Binding sitei238 – 2381NAD(P)HXBy similarity
    Metal bindingi241 – 2411PotassiumBy similarity
    Binding sitei374 – 3741FMNBy similarity
    Binding sitei377 – 3771FMN; via amide nitrogenBy similarity
    Binding sitei379 – 3791SubstrateBy similarity
    Binding sitei396 – 3961FMNBy similarity
    Binding sitei436 – 4361SubstrateBy similarity
    Binding sitei440 – 4401SubstrateBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi389 – 3902FMNBy similarity
    Nucleotide bindingi453 – 4542FMNBy similarity

    GO - Molecular functioni

    1. FMN binding Source: InterPro
    2. isomerase activity Source: UniProtKB-KW
    3. metal ion binding Source: UniProtKB-KW
    4. pyridoxamine-phosphate oxidase activity Source: TAIR

    GO - Biological processi

    1. pyridoxal metabolic process Source: TAIR
    2. pyridoxal phosphate biosynthetic process Source: GOC
    3. pyridoxine biosynthetic process Source: UniProtKB-KW

    Keywords - Molecular functioni

    Isomerase, Oxidoreductase

    Keywords - Biological processi

    Pyridoxine biosynthesis

    Keywords - Ligandi

    Flavoprotein, FMN, Metal-binding, NAD, Nucleotide-binding, Potassium

    Enzyme and pathway databases

    BioCyciARA:AT5G49970-MONOMER.
    MetaCyc:MONOMER-17901.
    UniPathwayiUPA00190; UER00304.
    UPA00190; UER00305.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic
    Short name:
    AtPPOX1
    Including the following 2 domains:
    Alternative name(s):
    PNP/PMP oxidase
    Short name:
    PNPOx
    Pyridoxal 5'-phosphate synthase
    Probable NAD(P)HX epimerase (EC:5.1.99.-)
    Gene namesi
    Name:PPOX1
    Synonyms:PDX3, PDXH
    Ordered Locus Names:At5g49970
    ORF Names:K9P8.11
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 5

    Organism-specific databases

    TAIRiAT5G49970.

    Subcellular locationi

    Plastidchloroplast 1 Publication

    GO - Cellular componenti

    1. chloroplast Source: TAIR
    2. cytosol Source: TAIR

    Keywords - Cellular componenti

    Chloroplast, Plastid

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 6363ChloroplastSequence AnalysisAdd
    BLAST
    Chaini64 – 530467Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplasticPRO_0000420549Add
    BLAST

    Proteomic databases

    PRIDEiQ9LTX3.

    Expressioni

    Tissue specificityi

    Expressed in leaves, stems, flowers and roots.1 Publication

    Inductioni

    Circadian regulation. Up-regulated by light, heat, jasmonic acid, ethylene and abscisic acid treatments. Down-regulated by drought and salt treatment. Not induced by UV irradiation.1 Publication

    Gene expression databases

    GenevestigatoriQ9LTX3.

    Interactioni

    Subunit structurei

    Homodimer.By similarity

    Protein-protein interaction databases

    STRINGi3702.AT5G49970.1-P.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9LTX3.
    SMRiQ9LTX3. Positions 73-309, 337-530.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini81 – 297217YjeF N-terminalAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni131 – 1355NAD(P)HXBy similarity
    Regioni200 – 2067NAD(P)HXBy similarity
    Regioni321 – 3244Substrate bindingBy similarity
    Regioni505 – 5073Substrate bindingBy similarity

    Domaini

    Most plant PPOX proteins have both a pyridoxamine 5'-phosphate oxidase domain and an extra YjeF N-terminal domain.

    Sequence similaritiesi

    In the N-terminal section; belongs to the NnrE/AIBP family.Curated
    In the C-terminal section; belongs to the pyridoxamine 5'-phosphate oxidase family.Curated
    Contains 1 YjeF N-terminal domain.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0259.
    HOGENOMiHOG000243404.
    InParanoidiQ9LTX3.
    KOiK00275.
    K17759.
    OMAiCVRIGKP.
    PhylomeDBiQ9LTX3.

    Family and domain databases

    Gene3Di2.30.110.10. 1 hit.
    3.40.50.10260. 1 hit.
    HAMAPiMF_01629. PdxH.
    MF_01966. NADHX_epimerase.
    InterProiIPR000659. Pyridox_Oxase.
    IPR019740. Pyridox_Oxase_CS.
    IPR011576. Pyridox_Oxase_FMN-bd.
    IPR021198. Pyridox_Oxase_pln.
    IPR019576. Pyridoxamine_oxidase_dimer_C.
    IPR012349. Split_barrel_FMN-bd.
    IPR004443. YjeF_N_dom.
    [Graphical view]
    PfamiPF10590. PNPOx_C. 1 hit.
    PF01243. Pyridox_oxidase. 1 hit.
    PF03853. YjeF_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037048. PyrdxN_5-P_Oxase_ross-cont_pln. 1 hit.
    SUPFAMiSSF50475. SSF50475. 1 hit.
    SSF64153. SSF64153. 1 hit.
    TIGRFAMsiTIGR00558. pdxH. 1 hit.
    TIGR00197. yjeF_nterm. 1 hit.
    PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
    PS51385. YJEF_N. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9LTX3-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MRNVIRRVTT MTFTFLLQSP PLPISPSPPQ FSLSSSPLSK TQRFITPSQG    50
    SRLRTLCTKV IIPNMQDSGS PPLSYLTQRE AAEIDETLMG PLGFSIDQLM 100
    ELAGLSVAAS IAEVYKPEEY SRVLAICGPG NNGGDGLVAA RHLHHFGYKP 150
    FICYPKRTAK PLYTGLVTQL DSLSVPFVSV EDLPDDLSKD FDVIVDAMFG 200
    FSFHGAPRPP FDDLIRRLVS LQNYEQTLQK HPVIVSVDIP SGWHVEEGDH 250
    EDGGIKPDML VSLTAPKLCA KRFRGPHHFL GGRFVPPSVA EKYKLELPSY 300
    PGTSMCVRIG KPPKVDISAM RVNYVSPELL EEQVETDPTV QFRKWFDEAV 350
    AAGLRETNAM ALSTANKDKK PSSRMVLLKG FDENGFVWFT NYESKKGSDL 400
    SENPSAALLF YWEILNRQVR IEGPVERIPE SESENYFHSR PRGSQIGAIV 450
    SKQSSVVPGR HVLYDEYEEL TKQYSDGSVI PKPKNWGGFR LKPNLFEFWQ 500
    GQPSRLHDRL QYSLQDVNGN PAWKIHRLAP 530
    Length:530
    Mass (Da):59,376
    Last modified:October 1, 2000 - v1
    Checksum:i22E8DFEC1A2167EE
    GO
    Isoform 2 (identifier: Q9LTX3-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         261-271: Missing.
         478-530: Missing.

    Note: Not detected in roots.

    Show »
    Length:466
    Mass (Da):52,042
    Checksum:i3E2B851F982461E5
    GO

    Sequence cautioni

    The sequence AAM65907.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
    The sequence AAM83249.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti241 – 2411S → Y in AAM65907. 1 PublicationCurated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei261 – 27111Missing in isoform 2. CuratedVSP_044534Add
    BLAST
    Alternative sequencei478 – 53053Missing in isoform 2. CuratedVSP_044535Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB024032 Genomic DNA. Translation: BAA97018.1.
    CP002688 Genomic DNA. Translation: AED95879.1.
    CP002688 Genomic DNA. Translation: AED95878.1.
    AY127025 mRNA. Translation: AAM83249.1. Different initiation.
    BT000605 mRNA. Translation: AAN18174.1.
    AY088368 mRNA. Translation: AAM65907.1. Different initiation.
    RefSeqiNP_568717.2. NM_124376.3. [Q9LTX3-1]
    NP_974918.1. NM_203189.1. [Q9LTX3-2]
    UniGeneiAt.28155.

    Genome annotation databases

    EnsemblPlantsiAT5G49970.1; AT5G49970.1; AT5G49970. [Q9LTX3-1]
    GeneIDi835061.
    KEGGiath:AT5G49970.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB024032 Genomic DNA. Translation: BAA97018.1 .
    CP002688 Genomic DNA. Translation: AED95879.1 .
    CP002688 Genomic DNA. Translation: AED95878.1 .
    AY127025 mRNA. Translation: AAM83249.1 . Different initiation.
    BT000605 mRNA. Translation: AAN18174.1 .
    AY088368 mRNA. Translation: AAM65907.1 . Different initiation.
    RefSeqi NP_568717.2. NM_124376.3. [Q9LTX3-1 ]
    NP_974918.1. NM_203189.1. [Q9LTX3-2 ]
    UniGenei At.28155.

    3D structure databases

    ProteinModelPortali Q9LTX3.
    SMRi Q9LTX3. Positions 73-309, 337-530.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 3702.AT5G49970.1-P.

    Proteomic databases

    PRIDEi Q9LTX3.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT5G49970.1 ; AT5G49970.1 ; AT5G49970 . [Q9LTX3-1 ]
    GeneIDi 835061.
    KEGGi ath:AT5G49970.

    Organism-specific databases

    TAIRi AT5G49970.

    Phylogenomic databases

    eggNOGi COG0259.
    HOGENOMi HOG000243404.
    InParanoidi Q9LTX3.
    KOi K00275.
    K17759.
    OMAi CVRIGKP.
    PhylomeDBi Q9LTX3.

    Enzyme and pathway databases

    UniPathwayi UPA00190 ; UER00304 .
    UPA00190 ; UER00305 .
    BioCyci ARA:AT5G49970-MONOMER.
    MetaCyc:MONOMER-17901.

    Gene expression databases

    Genevestigatori Q9LTX3.

    Family and domain databases

    Gene3Di 2.30.110.10. 1 hit.
    3.40.50.10260. 1 hit.
    HAMAPi MF_01629. PdxH.
    MF_01966. NADHX_epimerase.
    InterProi IPR000659. Pyridox_Oxase.
    IPR019740. Pyridox_Oxase_CS.
    IPR011576. Pyridox_Oxase_FMN-bd.
    IPR021198. Pyridox_Oxase_pln.
    IPR019576. Pyridoxamine_oxidase_dimer_C.
    IPR012349. Split_barrel_FMN-bd.
    IPR004443. YjeF_N_dom.
    [Graphical view ]
    Pfami PF10590. PNPOx_C. 1 hit.
    PF01243. Pyridox_oxidase. 1 hit.
    PF03853. YjeF_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF037048. PyrdxN_5-P_Oxase_ross-cont_pln. 1 hit.
    SUPFAMi SSF50475. SSF50475. 1 hit.
    SSF64153. SSF64153. 1 hit.
    TIGRFAMsi TIGR00558. pdxH. 1 hit.
    TIGR00197. yjeF_nterm. 1 hit.
    PROSITEi PS01064. PYRIDOX_OXIDASE. 1 hit.
    PS51385. YJEF_N. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones."
      Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H., Tabata S.
      DNA Res. 7:31-63(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    2. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    3. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 12-530 (ISOFORM 1).
      Strain: cv. Columbia.
    4. "Full-length cDNA from Arabidopsis thaliana."
      Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
      Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 34-530 (ISOFORM 1).
    5. "Identification of a pyridoxine (pyridoxamine) 5'-phosphate oxidase from Arabidopsis thaliana."
      Sang Y., Barbosa J.M., Wu H., Locy R.D., Singh N.K.
      FEBS Lett. 581:344-348(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE, CATALYTIC ACTIVITY.
    6. "Vitamer levels, stress response, enzyme activity, and gene regulation of Arabidopsis lines mutant in the pyridoxine/pyridoxamine 5'-phosphate oxidase (PDX3) and the pyridoxal kinase (SOS4) genes involved in the vitamin B6 salvage pathway."
      Gonzalez E., Danehower D., Daub M.E.
      Plant Physiol. 145:985-996(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE, CATALYTIC ACTIVITY.
    7. "Expression, in vivo localization and phylogenetic analysis of a pyridoxine 5'-phosphate oxidase in Arabidopsis thaliana."
      Sang Y., Locy R.D., Goertzen L.R., Rashotte A.M., Si Y., Kang K., Singh N.K.
      Plant Physiol. Biochem. 49:88-95(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY, INDUCTION, ALTERNATIVE SPLICING, SUBCELLULAR LOCATION.

    Entry informationi

    Entry nameiPPOX1_ARATH
    AccessioniPrimary (citable) accession number: Q9LTX3
    Secondary accession number(s): F4K7H2, Q8L7T7, Q8L9L3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 9, 2013
    Last sequence update: October 1, 2000
    Last modified: October 1, 2014
    This is version 102 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Mutants with reduced expression of PPOX1 (RNAi) have lower levels of total B6 vitamers, a reduced growth and are sensitive to high light.1 Publication

    Keywords - Technical termi

    Complete proteome, Multifunctional enzyme, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3